HISAT2 running pair end

Question

[catagui]

Hi is my first time to use HISAT2 but it does not want to run. I just get:

Warning: Could not open read file "S1_F_paired.fq" for reading; skipping...

I understand that by adding -q it should read the .fq files. Do I need to change my files names to 1.fq and 2.fq to each of my sample reads? I have 48 samples in pairs.

/space/home/aguilar/Programs/hisat2-2.1.0/hisat2 -x /space/home/aguilar/Ofav_temp/HiSat/Ofav -q -1 S1_F_paired.fq,S10_F_paired.fq,S11_F_paired.fq,S12_F_paired.fq -2 S1_R_paired.fq,S10_R_paired.fq,S11_R_paired.fq,S12_R_paired.fq -S /space/home/aguilar/Ofav_temp/HiSat/Ofav.sam

Thanks,

Catalina

Answer 1

[biplab]

I would try changing the file name to 'S1_F_paired_R1.fq' for R1 read and 'S1_F_paired_R2.fq' for R2 read.

[catagui]

Thanks, it seems that the program only reads the 1.fq or 2.fq for pair-reads. I wanted to make sure this is the case before editing all my files.